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Zinc in PDB 4oc4: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc4 was solved by J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.Pomper, J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.66
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.441, 130.459, 159.063, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Other elements in 4oc4:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine also contains other interesting chemical elements:

Iodine (I) 1 atom
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine (pdb code 4oc4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine, PDB code: 4oc4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4oc4

Go back to Zinc Binding Sites List in 4oc4
Zinc binding site 1 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:23.4
occ:1.00
O A:HOH1259 2.0 20.6 1.0
NE2 A:HIS553 2.1 19.0 1.0
OD2 A:ASP387 2.1 23.2 1.0
OE2 A:GLU425 2.1 21.2 1.0
OE1 A:GLU425 2.5 19.9 1.0
OAC A:2QN818 2.6 21.0 1.0
CD A:GLU425 2.6 20.4 1.0
CE1 A:HIS553 3.0 21.5 1.0
CG A:ASP387 3.0 21.2 1.0
CD2 A:HIS553 3.1 18.2 1.0
ZN A:ZN815 3.3 21.9 1.0
OD1 A:ASP387 3.3 21.1 1.0
CBA A:2QN818 3.4 23.3 1.0
CBG A:2QN818 3.9 22.7 1.0
NAX A:2QN818 4.0 21.7 1.0
CE1 A:TYR552 4.0 20.8 1.0
OE1 A:GLU424 4.1 19.7 1.0
ND1 A:HIS553 4.1 19.0 1.0
CG A:GLU425 4.1 20.9 1.0
O A:HOH916 4.2 22.3 1.0
CG A:HIS553 4.2 20.1 1.0
N A:2QN818 4.2 22.4 1.0
CB A:ASP387 4.3 22.0 1.0
OH A:TYR552 4.4 22.8 1.0
CA A:2QN818 4.5 23.2 1.0
NE2 A:HIS377 4.6 20.4 1.0
CZ A:TYR552 4.6 20.5 1.0
CAZ A:2QN818 4.6 25.8 1.0
CD1 A:TRP381 4.6 21.4 1.0
CE1 A:HIS377 4.8 19.4 1.0
NE1 A:TRP381 4.8 22.3 1.0
OD2 A:ASP453 4.9 21.1 1.0
OAF A:2QN818 4.9 24.6 1.0
CD1 A:TYR552 5.0 21.9 1.0
O A:HOH1256 5.0 28.3 1.0

Zinc binding site 2 out of 2 in 4oc4

Go back to Zinc Binding Sites List in 4oc4
Zinc binding site 2 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Cpibzl, A Urea-Based Inhibitor N~2~-{[(1S)-1-Carboxy-2- (Pyridin-4-Yl)Ethyl]Carbamoyl}-N~6~-(4-Iodobenzoyl)-L-Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:21.9
occ:1.00
OD1 A:ASP387 1.9 21.1 1.0
OD2 A:ASP453 1.9 21.1 1.0
O A:HOH1259 2.0 20.6 1.0
NE2 A:HIS377 2.0 20.4 1.0
CG A:ASP453 2.7 22.2 1.0
OD1 A:ASP453 2.8 24.3 1.0
CG A:ASP387 2.9 21.2 1.0
CE1 A:HIS377 3.0 19.4 1.0
CD2 A:HIS377 3.0 19.7 1.0
OD2 A:ASP387 3.2 23.2 1.0
ZN A:ZN814 3.3 23.4 1.0
OE2 A:GLU425 3.6 21.2 1.0
OE1 A:GLU424 3.6 19.7 1.0
CD A:GLU424 4.1 20.2 1.0
ND1 A:HIS377 4.1 20.4 1.0
CB A:ASP453 4.2 20.9 1.0
CG A:HIS377 4.2 18.6 1.0
CB A:ASP387 4.2 22.0 1.0
ND2 A:ASN519 4.2 19.8 1.0
CB A:PRO388 4.3 19.9 1.0
OE2 A:GLU424 4.3 20.8 1.0
CD A:GLU425 4.3 20.4 1.0
CA A:ASP387 4.5 21.1 1.0
CA A:PRO388 4.6 20.0 1.0
OAC A:2QN818 4.6 21.0 1.0
CBA A:2QN818 4.6 23.3 1.0
C A:ASP387 4.6 21.5 1.0
N A:PRO388 4.7 20.7 1.0
N A:2QN818 4.7 22.4 1.0
O A:HOH1256 4.7 28.3 1.0
OE1 A:GLU425 4.7 19.9 1.0
OG A:SER454 4.7 20.3 0.8
CA A:2QN818 4.9 23.2 1.0
OXT A:2QN818 4.9 23.2 1.0
NAX A:2QN818 5.0 21.7 1.0
CG A:GLU424 5.0 18.2 1.0

Reference:

J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.G.Pomper, J.Lubkowski, C.Barinka. Structural Characterization of P1'-Diversified Urea-Based Inhibitors of Glutamate Carboxypeptidase II. Bioorg.Med.Chem.Lett. V. 24 2340 2014.
ISSN: ISSN 0960-894X
PubMed: 24731280
DOI: 10.1016/J.BMCL.2014.03.066
Page generated: Sun Oct 27 03:40:01 2024

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